makenucseq Wiki The master copies of EMBOSS documentation are available at http://emboss.open-bio.org/wiki/Appdocs on the EMBOSS Wiki. Please help by correcting and extending the Wiki pages. Function Create random nucleotide sequences Description makenucseq writes an output file with a set of random nucleotide sequences. The sequence composition is defined from reading a codon usage file: the sequences are created with triplet frequencies matching those given in the file, with the end trimmed to be in the correct reading frame. The number of sequences to create and length of each sequence is specified. Optionally, a user-defined string may be inserted into each output sequence at a specified position Algorithm Usage Here is a sample session with makenucseq % makenucseq Create random nucleotide sequences Codon usage file (optional): Number of sequences created [100]: Length of each sequence [100]: nucleotide output sequence(s) [makeseq.fasta]: Go to the output files for this example Example 2 Providing a codon usage file specifies the sequence composition. This Pseudomonas aeruginosa file specifies a high GC content. % makenucseq Create random nucleotide sequences Codon usage file (optional): Epseae.cut Number of sequences created [100]: Length of each sequence [100]: nucleotide output sequence(s) [makeseq.fasta]: Go to the output files for this example Command line arguments Create random nucleotide sequences Version: EMBOSS:6.4.0.0 Standard (Mandatory) qualifiers (* if not always prompted): -codonfile codon Optional codon usage file. Nucleotide sequences will be created as triplets matching the frequencies in the file, with the end trimmed to be in the correct reading frame. -amount integer [100] Number of sequences created (Integer 1 or more) -length integer [100] Length of each sequence (Integer 1 or more) * -insert string String that is inserted into sequence (Any string) * -start integer [1] Start point of inserted sequence (Integer 1 or more) [-outseq] seqoutall [.] Nucleotide sequence set(s) filename and optional format (output USA) Additional (Optional) qualifiers: -useinsert toggle [N] Do you want to make an insert Advanced (Unprompted) qualifiers: (none) Associated qualifiers: "-codonfile" associated qualifiers -format string Data format "-outseq" associated qualifiers -osformat1 string Output seq format -osextension1 string File name extension -osname1 string Base file name -osdirectory1 string Output directory -osdbname1 string Database name to add -ossingle1 boolean Separate file for each entry -oufo1 string UFO features -offormat1 string Features format -ofname1 string Features file name -ofdirectory1 string Output directory General qualifiers: -auto boolean Turn off prompts -stdout boolean Write first file to standard output -filter boolean Read first file from standard input, write first file to standard output -options boolean Prompt for standard and additional values -debug boolean Write debug output to program.dbg -verbose boolean Report some/full command line options -help boolean Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose -warning boolean Report warnings -error boolean Report errors -fatal boolean Report fatal errors -die boolean Report dying program messages -version boolean Report version number and exit Input file format makenucseq reads an optional codon usage file. The input is a standard EMBOSS codon usage query. Data can also be read from codon usage output in any supported format written by an EMBOSS or third party application. The input format can be specified by using the command-line qualifier -format xxx, where 'xxx' is replaced by the name of the required format. The available format names are: emboss, cut, gcg, cutg, cutgaa, spsum, cherry, transterm, codehop, staden and numstaden. Output file format makenucseq writes a sequence file with the number of sequences requested. Output files for usage example File: makeseq.fasta >EMBOSS_001 ggtccgaggggtagcttgatcgcctcttttgggaacgcaagcgtggccggtatgataaaa taaaatgcgctccgctctggtaagacggacggtcgcccta >EMBOSS_002 tttcaatccattaggagatccttccgggcttactcttttttggtaggaatacagacgaat gtgttgttgacactacaagtacgaactgtgatcgcaccct >EMBOSS_003 aacggctgttagaccgcatcattttggcaggaaccttgggtcggttcatctcttgggtat gacagcacagggaggtttgagagctgcctcccggattttg >EMBOSS_004 atcgaagagacgcattcctatagtatcaatccttgacgtcggcatggttcggatcttacg cgaagccctacgactccctaccggtattgtatcgttctag >EMBOSS_005 agagttcgtctacacatgggcacccttactacttgagtgcttaccaaaagtacgatccac gaaacgtcgagcactggcatgcacacgctctccgacgtat >EMBOSS_006 caatcctcattgcttacacggccacaacaggaagtgcctcaagctgtagagcataggcat gttctcaagatcgcgttaacagccattgctggagaatggc >EMBOSS_007 actcggagttcaaccgccgctgtgggctgagctatccctaatgacccgcgcgtagagtgt taaaatctttcgacagtcacctgcacatcgttgtcttctg >EMBOSS_008 cgagggtcattctaaatttgagggtaatgctcgcgccatgcgacttgtcgggaaagcggc cctttatgcgttgccggtcggcattgcccaaccctagtga >EMBOSS_009 gttatcacgtccaattaggtgggccacaatacgtcggcagaatcaagtgcataacggaga ggtcactaggacgttactgtcattccctgccccgctatgt >EMBOSS_010 tatgtttctcgtgctcagcttagaccggagagctccacccaataggccgcacacaagggg tctttaggatacccccccccttattaccccacagcaacag >EMBOSS_011 agacgcgccgctcgtagtatgttacctcccttacctgaggacctgcgtggatggcggcaa cgtgcctcaaagcccgcagcgaatggaaagcaggttggtg >EMBOSS_012 accctcgcgctgtcgtgtatatttctagcgatgagctagttcgtgcggccatggttctgg atgcatggctatggtttgttcagacggaatagtccgggac >EMBOSS_013 accctgacagctcttaccctctatggacggacagggcatgaccgtgcatgacctggcaga gaacggcttcatattagggagcagcagaatcgtgtatcgt >EMBOSS_014 tcctgccgggaattagagacaaaaagattgtgaccttcacagcctcctactttcttttgt tagtatggggcttgacactatacactgggacaatttagaa >EMBOSS_015 ccgtagcaaggccacagttacgaaggtcatgttcccacccacagcgttgttcccttttac cgacccacgcctagaatttctcgaagaacagaaaccaccc >EMBOSS_016 cttctcccgtaagaaccttcgtccaacatccaatcaatcacggtgggtacgaggtatacc tatctgtcacgaaatcctaagacatttctgcaaacagggg >EMBOSS_017 cagtagttgatgcacgtaacatttactcattggacaacagcacagtagctcccatcacat [Part of this file has been deleted for brevity] >EMBOSS_084 ttaccatttaaacatgtccagatacggacaggtcgcactgtccttgggccacttttctgt tacgcgcgtgagcttatgatgacgaatcgcgggaagggat >EMBOSS_085 cctcactctctcagaccccgaatcctaagtgatcaatacctctacgtcttggttttgccg ctgatatcatgatatacatgagtctagcacggtctcctac >EMBOSS_086 aggcagggtatagtgctctagagtacaccccttgcgtgaaatcggcgtcctggtggtcga ttaccctcaagcacttttcctcagttcggggggtcacgat >EMBOSS_087 ataagtctaccaatgaaacgatcgcgaatcggacgccactcgccagggtattcgcgcttc acattatatatagtccggaagcacgactctccatttggtt >EMBOSS_088 tctatccgtgcctcccacgggtcagatatatgctctggacgtagtggtgccgcatctgtg tacatgactaaagctacgactttttcgcgtagccaatcca >EMBOSS_089 ccgccgtaactttcccgggtagggggctaccgacgataatctagcgtttgatagcgtctg gcgcatgtgtcatagggtgctggtgtccttgggcagtaca >EMBOSS_090 acgaatccccctttccacacgacaaaaacgagaccggtagctttgggcgagacgtacgct gactaagcaatcgaagcccttcaagtacgctgccagtcaa >EMBOSS_091 gtgacctgagacttgagctactaatgcacttgtacgagggcttacaaaaagaacggatca aagcaagccctcgggatgtgtgacccaggcgtttgccgtg >EMBOSS_092 accgttcgagagatctcacaactagcacatatacgccagaggtagtcacacagattaaga tggtgcgacagctcgcgcaaccacacggggatgacacgta >EMBOSS_093 aaccctaaccgagggtttgtggctaacatcagccccactgtgcccgcaacgtcccaaatt gactctatctcgttccaacactttaaatgcttatgtatat >EMBOSS_094 gtctggtacgttcagcgcgattagccgggcgctccggaccggatgtcctaccaggtacac ctatccagtaccacggcgcggtgtagccgtacctcaaagc >EMBOSS_095 taggttggatagacgacggtctgtcaaggctcaccaagggttaatctgcctctgataagt gttggactatgggggcaacgcctcgaccagttgaacctgt >EMBOSS_096 gaccgtggtgcattctagtacgtatgagcatccaaacatgcgccacatgtaccagggtga tgctggagtcgctgtggaacaagagcgttctaccccctcg >EMBOSS_097 atcataggcccaagtcggatcatgtttatccgagtttaacaagttctgcagtggcagaaa agtgtctttttagcagctcccctattgccacggctgctac >EMBOSS_098 taactagcagtttcgttatttaagagacttatgcgttaataaaatcttgttatggggcca ccagtccttattaatccgtaaggagacgagccgcctggag >EMBOSS_099 tcgggatgggaactgtagtaagtaaatacagcagaacaagaccagctgtaggaccgcaag taattcgcatggggccttgctctctacaatcacggcagcc >EMBOSS_100 taaatcggcatggtggagttatctttaagattgcaccatatgtggccgagccggaaaagc ttatggggtgccaggtttagcctcttgttacatagtgacg Output files for usage example 2 File: makeseq.fasta >EMBOSS_001 gggcgtctgggcgccgtcacggtcggccgctacctcgacccggcgttctccgtcaacttc gcgcggcagggcttcatctgactgctgttcggcgtgcgcg >EMBOSS_002 gacgccggcgcgaccgagcggcaccgcttcgtccgaggaggcggcggcttcaccctcgtg gccttcgacgacagcaccctggaagagaaggactacccgg >EMBOSS_003 cgcgccttcgccgccggtggcctgcactggggggttctgaccgagggcaggatcggccgc aggggcccggtgctgatcgtcgcccaccacctgaccctgc >EMBOSS_004 ctgcagaaggacttaatgcacaccctgttcaagcggggtaaacccgagctgggcatcctg ttcggccagcgcgtgccggccttgtcgaccggctacggcc >EMBOSS_005 ttcctctcctacctgcgctacctgaacgtgccagaagagtccagcggcgaacgcagcgcc ggcaccgacctgcgctcccccttcctgcggctgtgaggtg >EMBOSS_006 gccgacgcgtgcgaccataccgaccgcctggacatccgcagcaccatgttccccctgcgc gagctcatccgcgcggaggcgatcatctacgacgagggcg >EMBOSS_007 ccgcacctgcgcctgctgaccgtgaacgccattccggccaattggatcacctcgtgcctg ctggtgggcatcaagggcgggaccgaggccggcttcctgg >EMBOSS_008 ggcggcctggcgcctcgctatcgtgccaactgcatcttcgcgctgctgcggcggccgctg gacctgccggatgcggaggtcgccgagagtgacccggttg >EMBOSS_009 aagggcccgctgctctcagggaacgtcacgcgcgcgtacgtcggcgcggaagccgccgcg gttgtggccctgtcgctgctgcgggactatgccgtagaga >EMBOSS_010 gtcgacggtaaggccgtggcgacctcgttccaggccctggaacttgagggctccacctcg ggaaaagagctgatgatccgttacgtaagcggccgccgtc >EMBOSS_011 cggcgcgcggcactcccggtctcgttcgccccgcggaactggcacctgtggacgatccgc caagtcgagaagtaaggccacgccctcacgggccgcaaga >EMBOSS_012 tatcaggcccagctcgagcaacaccatccgtgcagctgactcggccgtaattggcagcat ctttcgatcttggccccgaagggtaagcgcttgctggcgg >EMBOSS_013 ctgatctacacccatgcccagaccctagtgggcccgcacaaggcgcaccaacgttgaact ggctgagaccagtgggaaccgaaacgctacgggggcctcc >EMBOSS_014 gccatggccaccaacgaagatggctgcgccatccgcagcctccagcaggacgcgggcgag acggaccaaccgctgcacggcgacgtgatgaacattttcg >EMBOSS_015 cgccagagctcgcgcggcgaggcgacccagggcgcgctgcagtggggacaggtcaacgcg ccgctggacttcgcgagcaacctgcagatgctcattgagc >EMBOSS_016 ctgggcgcgtcgctggagggcgaccacggcgtggcgcagaaagctaatgccagtgatggt gtcgatacccgactgcctgcgatgtgggccgacaagccga >EMBOSS_017 ctcggcttcagccccacccctgcgagcctggacgtgggcgctaagttcggcctctcgggc [Part of this file has been deleted for brevity] >EMBOSS_084 ctgcgccacctgcgcggggaaaacggcatcgccacgatgtcggagatcggtgagtacgcg agcaagcggggcatggaagccgaggccttcctgagcacac >EMBOSS_085 cactactacatccgcctgctgctgcaggccaccatcttcctggtcagccgcacgcgcacc ggcgtattgattatctgtcgctttgagccggtgtttaaga >EMBOSS_086 actgccgagatcaagcagtacggtgcgccgccggcaccgggtgacgccctcggcgaccgc gactgccgcggcgccgtgggtctgctgagccgccaatccg >EMBOSS_087 cggaggaacaccagcgacatctatgaatggttcctgcagctggccaccgtgtcgctgatc gccgaggagctcatcaacttccgtaccggccagaatgccc >EMBOSS_088 gggatcctggacgaagcggccgccttctcgaaggagaacagaagctactatccggacggc ctgtacacccacgtgtacaagcgcaacgagcaatggcgga >EMBOSS_089 gcgctgctgcgcgcccgctcgaaatgggatcgctacgagaacatcgccaagtacctgatg aaggaggaggcagacgccgaccaggaacaggtcaccctcc >EMBOSS_090 ccgatcgacggctacggtaccaacctgtacgccccgatgccgcatctgggcaggagcgac cccccgcgcgccctcgggcccccaattcaacagatcgctc >EMBOSS_091 gcgaaccactcgaacgttctggtgatggcgcataccaattacaaccgcgacgccggccgt atcccctaccaaccgagtcgacacaccggcgaggccggcg >EMBOSS_092 tccatcgagaaggccatcccgccggtccgtatcaaggggctggccggccgcccgtgcctc ctaggccgggcgagcctagcgaccatcgcctatgacgcca >EMBOSS_093 attctgcccgacgaagacctctacgagatccgcggcttcatgcacaaggccgggcatgcg gacccgggcgacgaacatatcaccgtgccgctcaggcacc >EMBOSS_094 cgcgtctacccgcgtcaggacgcgctgaccgccgtcctggtgaaccgccttgacaatttc ctgaccctgggcaaccagatgctggagctcaacgtccaat >EMBOSS_095 gacctgatggagcatttcagctcgtacctgtccctggccggcggcctcttaggcataaag cgcaccgccccgctatcccgtatcgggacggccctggata >EMBOSS_096 tgactggtcagctacggccgcttcctgctcatcgccccgctgggtctgcggacggagttc gaacagctgtccctgggcggcgagccgggcccggccgacc >EMBOSS_097 gcccatcggggtcgctgcgtgaatccgtgcgttggagcgcggcgcgcctgcgaaaacctg ccgctgtcgccggcggtgctgctggaggtggtccgcagcg >EMBOSS_098 cgcgcccctatggaacgcctgttcgcggcgttcgcgatcgccatcctggggatcatggtg ttcgccatgctggacatcagcatcgaagagcgtttcccgc >EMBOSS_099 gcgaagtgccgcaccttcgtgggcagctacacgattcagagtttggacacccgggagacg aagcagaccgtcatcgatgaggagaccaagaccaaattga >EMBOSS_100 ctcggccggcaactgcggcgcgaaccgatgccgccctacgcggccctgcgttagatggac ctcgcccccgcccgcgaccgagtcgcgctcgacacggtcg Data files None. Notes None. References None. Warnings None. Diagnostic Error Messages None. Exit status It always exits with status 0. Known bugs None. See also Program name Description aligncopy Reads and writes alignments aligncopypair Reads and writes pairs from alignments biosed Replace or delete sequence sections codcopy Copy and reformat a codon usage table cutseq Removes a section from a sequence degapseq Removes non-alphabetic (e.g. gap) characters from sequences descseq Alter the name or description of a sequence entret Retrieves sequence entries from flatfile databases and files extractalign Extract regions from a sequence alignment extractfeat Extract features from sequence(s) extractseq Extract regions from a sequence featcopy Reads and writes a feature table featreport Reads and writes a feature table feattext Return a feature table original text listor Write a list file of the logical OR of two sets of sequences makeprotseq Create random protein sequences maskambignuc Masks all ambiguity characters in nucleotide sequences with N maskambigprot Masks all ambiguity characters in protein sequences with X maskfeat Write a sequence with masked features maskseq Write a sequence with masked regions newseq Create a sequence file from a typed-in sequence nohtml Remove mark-up (e.g. HTML tags) from an ASCII text file noreturn Remove carriage return from ASCII files nospace Remove whitespace from an ASCII text file notab Replace tabs with spaces in an ASCII text file notseq Write to file a subset of an input stream of sequences nthseq Write to file a single sequence from an input stream of sequences nthseqset Reads and writes (returns) one set of sequences from many pasteseq Insert one sequence into another revseq Reverse and complement a nucleotide sequence seqcount Reads and counts sequences seqret Reads and writes (returns) sequences seqretsetall Reads and writes (returns) many sets of sequences seqretsplit Reads sequences and writes them to individual files sizeseq Sort sequences by size skipredundant Remove redundant sequences from an input set skipseq Reads and writes (returns) sequences, skipping first few splitsource Split sequence(s) into original source sequences splitter Split sequence(s) into smaller sequences trimest Remove poly-A tails from nucleotide sequences trimseq Remove unwanted characters from start and end of sequence(s) trimspace Remove extra whitespace from an ASCII text file union Concatenate multiple sequences into a single sequence vectorstrip Removes vectors from the ends of nucleotide sequence(s) yank Add a sequence reference (a full USA) to a list file Author(s) This application was contributed by Henrikki Almusa, Medicel, Helsinki, Finland Please report all bugs to the EMBOSS bug team (emboss-bug (c) emboss.open-bio.org) not to the original author. History Target users This program is intended to be used by everyone and everything, from naive users to embedded scripts. Comments None